The partitioning and processing of species such as analytes and reagents is important for a variety of applications, including molecular biology applications and medical applications. Appropriate sample preparation is often needed prior to performing a reaction such as a polynucleotide sequencing reaction or an analyte detection reaction. For example, a sample such as a biological sample, including a collection of cells, tissue, and/or nucleic acids may need to be lysed, fragmented, or otherwise manipulated in order to permit downstream analysis. Sample preparation may also involve isolating certain molecules, and/or attaching unique identifiers to certain molecules, among other processes. There is a need in the art for improved methods, compositions, systems, devices, and kits for partitioning and processing of species.